Contacts of the strand formed by residues 127 - 134 (chain B) in PDB entry 3ZXR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.6 6.2 - - - +
125B ALA 3.8 0.8 - - - -
126B ASP* 1.3 95.0 + - - +
128B ALA* 1.3 62.5 + - - +
129B TYR* 3.6 39.2 + - + +
234B SER* 4.0 16.8 - - - -
280B SER 3.9 0.3 - - - +
281B LEU* 3.4 5.9 - - - +
282B TRP* 2.9 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 6.0 1.5 + - + +
119B LEU* 3.5 13.1 - - + +
127B THR* 1.3 73.7 - - - +
129B TYR* 1.3 62.0 + - - +
130B PHE* 3.7 20.3 - - + -
234B SER* 3.3 4.2 - - - -
235B LEU* 3.0 32.2 + - + -
280B SER 3.6 5.4 - - - +
281B LEU* 3.7 17.7 - - + -
305B TYR* 5.7 0.2 - - - +
384B LEU* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR* 3.6 25.5 + - + +
128B ALA* 1.3 71.3 - - - +
130B PHE* 1.3 63.7 + - - +
232B PHE* 3.6 35.2 - + + -
233B ASN* 3.4 22.0 - - - -
234B SER* 3.6 12.6 - - - -
278B HIS 3.5 0.5 - - - +
279B GLN* 3.4 8.7 - - - +
280B SER* 2.9 40.4 + - - +
282B TRP* 3.4 52.1 - + + -
501B IQ1 3.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA* 3.7 23.8 - - + -
129B TYR* 1.3 78.3 - - - +
131B GLY* 1.3 60.3 + - - +
132B ALA 4.1 1.3 + - - -
232B PHE* 3.4 4.5 - - - +
233B ASN 2.8 29.2 + - - +
235B LEU* 3.7 31.4 - - + -
238B ALA* 3.9 21.9 - - + +
277B CYS* 4.6 6.1 - - + -
278B HIS 3.4 2.9 - - - -
279B GLN* 3.7 35.9 - - + -
305B TYR* 4.4 8.1 - - - -
380B PHE* 3.5 59.5 - + + -
383B MET* 4.2 3.8 - - - -
384B LEU* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 1.3 73.4 - - - +
132B ALA* 1.3 60.9 + - - -
230B TYR 5.6 0.2 - - - -
232B PHE* 3.7 17.9 - - - -
276B HIS 3.5 1.2 - - - +
277B CYS* 3.4 3.1 - - - -
278B HIS* 2.7 45.3 + - - +
501B IQ1 3.6 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE 4.1 1.8 + - - -
131B GLY* 1.3 75.5 - - - -
133B GLU* 1.3 67.1 + - - +
134B ALA 3.9 1.6 + - - -
228B ILE 5.0 1.2 - - - +
229B ASN* 4.4 8.1 + - - -
230B TYR* 4.6 21.8 + - + +
238B ALA* 6.5 0.2 - - + -
242B MET* 3.3 31.2 - - + -
275B MET* 4.4 4.7 - - + -
276B HIS 3.3 6.7 - - - +
277B CYS* 4.8 2.5 - - - -
380B PHE* 4.2 17.9 - - + -
501B IQ1 4.0 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 1.3 78.3 - - - +
134B ALA* 1.3 59.4 + - - +
135B GLU* 3.4 3.8 + - + +
227B GLU* 2.9 19.7 - - - +
228B ILE 5.0 0.4 - - - -
229B ASN* 3.8 13.2 - - - +
274B GLY 2.9 16.5 - - - +
275B MET* 3.1 11.7 - - - -
276B HIS* 3.0 26.2 + - + +
278B HIS* 2.9 17.9 + - - -
366B GLU* 3.0 2.1 - - - +
501B IQ1 4.0 10.8 - - + -
503B MG 2.0 28.3 - - - -
504B MG 2.0 33.3 - - - -
505B P3S 2.9 2.8 + - - -
506B PO4 2.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA 3.9 2.4 + - - -
133B GLU* 1.3 70.1 - - - +
135B GLU* 1.3 64.7 + - - +
136B PHE* 3.6 5.5 - - - -
227B GLU* 5.3 1.8 - - - -
228B ILE 4.8 3.9 + - - +
230B TYR* 6.3 0.6 - - - -
242B MET* 3.6 26.2 - - + +
245B TYR* 2.9 48.9 + - + -
262B PHE* 3.7 5.8 - - + -
274B GLY 3.7 4.0 - - - -
275B MET* 4.4 1.6 - - + +
372B SER* 3.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il